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Benchmarking TriadAb using targets from the second antibody modeling assessment.

Frederick S Lee1, Amos G Anderson1, Barry D Olafson1

  • 1Protabit LLC, 111 Waverly Drive, Pasadena, CA 91105, USA.

Protein Engineering, Design & Selection : PEDS
|October 21, 2023
PubMed
Summary

The Triad Antibody Homology Modeling (TriadAb) package accurately predicts antibody Fv domain structures using template-based modeling. Its performance, validated against AMA-II, shows high accuracy for antibody engineering applications.

Keywords:
antibody homology modelingbenchmarkingprotein model quality

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Area of Science:

  • Computational biology
  • Structural biology
  • Immunology

Background:

  • Antibody therapeutics development relies heavily on computational modeling and design.
  • Accurate prediction of antibody structures is crucial for engineering novel therapeutic agents.

Purpose of the Study:

  • To introduce the Triad Antibody Homology Modeling (TriadAb) package for predicting antibody Fv domain structures.
  • To evaluate the performance and accuracy of TriadAb in antibody structure prediction.

Main Methods:

  • Utilized template-based homology modeling to predict antibody Fv domain structures from heavy and light chain sequences.
  • Benchmarked TriadAb's performance against results from the Second Antibody Modeling Assessment (AMA-II).

Main Results:

  • TriadAb achieved average main-chain carbonyl root-mean-square deviations of 1.10 Å (framework) and ranging from 1.27 Å to 3.04 Å across complementarity-determining regions (CDRs).
  • Results were comparable to those reported in AMA-II, demonstrating high accuracy.

Conclusions:

  • TriadAb provides sufficiently accurate and useful antibody models for engineering purposes.
  • The TriadAb package is a valuable tool for antibody engineering within the Triad protein design platform.